https://zenodo.org/record/1258475/files/article.pdf

Electron transfers in chemistry and biology

Signaling Recognition Events with Fluorescent Sensors and Switches.

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters are reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P, and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins. Bond stretch, angle bend, and torsional terms have been adopted from the AMBER united-atom force field. As reported here, further testing has involved studies of conformational energy surfaces and optimizations of the crystal structures for four cyclic hexapeptides and a cyclic pentapeptide. The average root-mean-square deviation from the X-ray structures of the crystals is only 0.17 A for the atomic positions and 3% for the unit cell volumes. A more critical test was then provided by performing energy minimizations for the complete crystal of the protein crambin, including 182 water molecules that were initially placed via a Monte Carlo simulation. The resultant root-mean-square deviation for the non-hydrogen atoms is still ca. 0.2 A and the variation in the errors for charged, polar, and nonpolar residues is small. Improvement is apparent over the AMBER united-atom force field which has previously been demonstrated to be superior to many alternatives. Computer simulations are undoubtedly destined to became an increasingly important means for investigating the structures and dynamics of biomolecular systems.' At the heart of such theoretical calculations are the force fields that describe the interatomic interactions and the mechanics of deformations of the molecules.* There is also little doubt that there will be a continual evolution in force fields with added complexity and improved performance paralleling the availability of computer resources. Our own efforts in this area over the last few years have resulted in the OPLS potential functions for proteins whose development and performance are summarized here. These potential functions have a simple form and they have been parametrized directly to reproduce experimental thermodynamic and structural data on fluids. Consequently, they are computationally efficient and their description of proteins in solution or crystalline environments should be superior to many alterantives that have been developed with limited condensed-phase data. The latter point is pursued here primarily through calculations on the crystal structures for four cyclic hexapeptides, a cyclic pentapeptide, and the protein crambin. Improvements are apparent in comparison to the AMBER united-atom force field3 which has previously been shown to be superior to many alternative^.^ (1) Beveridge, D. L., Jorgensen, W. L., Eds. Ann. N.Y. Acad. Sci. 1986, 482. ( 2 ) For reviews, see: (a) Levitt, M. Annu. Reu. Biophys. Eioeng. 1982, 11, 251. (b) McCammon, J. A. Rep. Prog. Phys. 1984, 47, 1. (3) Weiner, S. J.; Kollman, P. A.; Case, D. A,; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. SOC. 1984, 106, 765. Parametrization The peptide residues of proteins contain readily identifiable organic subunits such as amides, hydrocarbons, alcohols, thioethers, etc. In view of this and since data are available on the corresponding pure organic liquids, our approach to developing a force field for proteins was to build it up from parameters demonstrated to yield good descriptions of organic liquids. U1timately, the force field would need to treat both intramolecular terms for bond stretches, angle bends, and torsions, as well as the intermolecular and intramolecular nonbonded interactions. The latter are generally accepted to be the most difficult part of the problem and have been our focus.3 A simple, computationally efficient form was chosen to represent the nonbonded interactions through Coulomb and Lennard-Jones terms interacting between sites centered on nuclei (eq 1). Thus, the intermolecular inter-

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

Application of the pople-santry-segal CNDO method to the cyclopropylcarbinyl and cyclobutyl cation and to bicyclobutane

The Conservation of Orbital Symmetry

Intramolecular long-distance electron transfer (EI) has been actively studied in recent years in order to test existing theories in a quantitative way and to provide the necessary constants for predicting ET rates from simple structural parameters. Theoretical predictions of an "inverted region," where increasing the driving force of the reaction will decrease its rate, have begun to be experimentally confirmed. A predicted nonlinear dependence of ET rates on the polarity of the solvent has also been confirmed. This work has implications for the design of efficient photochemical charge-separation devices. Other studies have been directed toward determining the distance dependence of ET reactions. Model studies on different series of compounds give similar distance dependences. When different stereochemical structures are compared, it becomes apparent that geometrical factors must be taken into account. Finally, the mechanism of coupling between donor and acceptor in weakly interacting systems has become of major importance. The theoretical and experimental evidence favors a model in which coupling is provided by the interaction with the orbitals of the intervening molecular fragments, although more experimental evidence is needed.

https://science.sciencemag.org/content/sci/240/4851/440.full.pdf

Intramolecular Long-Distance Electron Transfer in Organic Molecules

A homologous series of eight compounds of the general structure A-Sp-B where B is 4-biphenylyl, Sp is a rigid saturated hydrocarbon spacer, the steroidal 5..cap alpha..-androstane skeleton, and A is one of a series of 8 different molecular groups with ..pi.. electron networks was synthesized. A liquid solution of these molecules in either 2-methyltetrahydrofuran or isooctane at room temperature was subjected to a 30-ps pulse of solvated electrons. Data are presented that demonstrate in these systems the dependence of the electron transfer rates on the exothermicity of the reaction and on solvent polarity. It is also noted that the electron transfer reactions are free ion reactions.

Intramolecular long-distance electron transfer in radical anions. The effects of free energy and solvent on the reaction rates

A series of molecules with the general structure A/sub 1/-Sp-A/sub 2/ have been synthesized. Pulse radiolysis was used to convert them into negative ions, and the rates of intramolecular electron transfer were measured. In the first series studied Sp is the androstane skeleton with the acceptors attached to the 3- and 16-positions. The series consisted of eight molecules with A/sub 2/ = 4-biphenyl and eight different A/sub 1/ groups differing in electron affinity by 2.4 eV. The electron transfer rates differ by more than 3 orders of magnitude throughout the series and depend in a very nonlinear fashion on the free energy of the reaction. The second series of molecules was designed to study the effect of the spacer which was varied from the steroid to decalins (eight compounds) and cyclohexanes (four compounds). No comprehensive distance dependence exists. Instead, the rates are strongly influenced by the donor-acceptor attachment geometry which influences the electronic coupling. For the type of spacers studied it was found that the electron transfer rates are slowed down by 1 order of magnitude for each 2.0 bonds for a constant reorganization energy.

Distance, stereoelectronic effects, and the Marcus inverted region in intramolecular electron transfer in organic radical anions

A model for polarized EPR spectra generated in radical pair reactions in micelles is being proposed. The model is based on electron spin-spin interactions which remain observable because of limited diffusion in micelles. The experimental observable is a doubling of hyperfine transitions, split by the magnitude of the interaction. The polarization is generated by the nonadiabatic generation of the radical pair with a triplet or singlet precursor. The time evolution of the wave function leads to a non-Boltzmann distribution of the populations among the four energy levels. The theory is tested by comparison with experiments, previously reported and repeated in this laboratory, obtained by laser flash photolysis of benzophenone in sodium dodecyl sulfate (SDS) micelles. Simulations of the shape of the spectra and their time dependence give excellent agreement with experiment. The model is further supported by experiments in micelles modified by different salt concentrations as well as different chain lengths of the micelle-forming molecules.

Gerhard L. Closs

Papers

Intramolecular Long-Distance Electron Transfer in Organic Molecules

Intramolecular long-distance electron transfer in radical anions. The effects of free energy and solvent on the reaction rates

Distance, stereoelectronic effects, and the Marcus inverted region in intramolecular electron transfer in organic radical anions

Spin-polarized electron paramagnetic resonance spectra of radical pairs in micelles: observation of electron spin-spin interactions

Mechanism explaining nuclear spin polarizations in radical combination reactions